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- PDB-6ozb: Crystal structure of the phycoerythrobilin-bound GAF domain from ... -

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Basic information

Entry
Database: PDB / ID: 6ozb
TitleCrystal structure of the phycoerythrobilin-bound GAF domain from a cyanobacterial phytochrome
ComponentsTwo-component sensor histidine kinase
KeywordsSIGNALING PROTEIN / cyanobacterial phytochromes / photoreceptors
Function / homology
Function and homology information


detection of visible light / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription
Similarity search - Function
Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal ...Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHYCOERYTHROBILIN / Two-component sensor histidine kinase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHeewhan, S. / Xiaoli, Z. / Yafang, S. / Zhong, R. / Wolfgang, G. / Kai, H.Z. / Xiaojing, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01EY024363 United States
Other privateCBC C-086 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome.
Authors: Slavov, C. / Fischer, T. / Barnoy, A. / Shin, H. / Rao, A.G. / Wiebeler, C. / Zeng, X. / Sun, Y. / Xu, Q. / Gutt, A. / Zhao, K.H. / Gartner, W. / Yang, X. / Schapiro, I. / Wachtveitl, J.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-component sensor histidine kinase
B: Two-component sensor histidine kinase
C: Two-component sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7786
Polymers69,0123
Non-polymers1,7663
Water12,448691
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-76 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.967, 78.967, 209.299
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1173-

HOH

21A-1178-

HOH

31A-1226-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: PEB / End label comp-ID: PEB / Auth seq-ID: 11 - 900 / Label seq-ID: 11

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - D
2chain BBB - E
3chain CCC - F

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Components

#1: Protein Two-component sensor histidine kinase


Mass: 23004.090 Da / Num. of mol.: 3 / Mutation: Y71H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all2699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YTL8
#2: Chemical ChemComp-PEB / PHYCOERYTHROBILIN / Phycoerythrobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium acetate, sodium citrate tribasic dihydrate. Crystal was set up under green safety light and grown in dark

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 61064 / % possible obs: 85.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.18 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.088 / Χ2: 1.267 / Net I/σ(I): 8.4 / Num. measured all: 274187
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.834.20.62925030.7740.3290.7130.76471.6
1.83-1.864.30.51925930.8220.2640.5850.78874.5
1.86-1.94.40.44228250.8810.2170.4940.83880.1
1.9-1.944.70.38328390.9090.1830.4260.85381.8
1.94-1.984.70.3328600.9330.1570.3670.88681
1.98-2.034.70.27828640.9530.1320.3090.88581.3
2.03-2.084.70.2429100.9630.1150.2670.92182.3
2.08-2.134.70.21128970.9710.1020.2350.94682.2
2.13-2.24.60.17429110.9780.0840.1940.97583.1
2.2-2.274.60.1629270.980.0770.1781.04883.4
2.27-2.354.50.1429460.9850.0680.1561.13683.8
2.35-2.444.50.12830120.9850.0620.1431.30184.7
2.44-2.554.40.11830270.9880.0570.1321.50185.2
2.55-2.694.30.09831070.9910.0480.111.58487.5
2.69-2.864.30.08731540.9930.0430.0971.58389
2.86-3.084.20.07533190.9940.0370.0841.6792.4
3.08-3.394.20.06634320.9940.0340.0751.80895.5
3.39-3.884.30.05634900.9950.030.0632.09396.8
3.88-4.884.50.04136130.9970.0210.0461.72398.4
4.88-504.90.03838350.9980.0190.0431.50799.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W2Z

3w2z


Resolution: 1.8→33.746 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 2011 3.3 %
Rwork0.1516 58980 -
obs0.153 60991 85.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.29 Å2 / Biso mean: 32.3019 Å2 / Biso min: 9.59 Å2
Refinement stepCycle: final / Resolution: 1.8→33.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 243 692 5327
Biso mean--25.55 36.04 -
Num. residues----565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134673
X-RAY DIFFRACTIONf_angle_d1.4046374
X-RAY DIFFRACTIONf_chiral_restr0.053748
X-RAY DIFFRACTIONf_plane_restr0.006824
X-RAY DIFFRACTIONf_dihedral_angle_d13.8661737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3265X-RAY DIFFRACTION7.941TORSIONAL
12B3265X-RAY DIFFRACTION7.941TORSIONAL
13C3265X-RAY DIFFRACTION7.941TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.84490.24291190.2195345772
1.8449-1.89480.25921310.1917378578
1.8948-1.95050.22981290.1774396782
1.9505-2.01350.24621350.173395581
2.0135-2.08540.18731290.1625397382
2.0854-2.16890.19071410.1552400783
2.1689-2.26760.22341390.1438404883
2.2676-2.38710.19231400.1462410084
2.3871-2.53660.1941370.1518416885
2.5366-2.73240.19851490.1525428287
2.7324-3.00720.1821510.1625444591
3.0072-3.4420.21561670.1549474695
3.442-4.33520.16271680.1297486097
4.3352-33.7460.18021760.1444518799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3388-0.17220.03672.1227-1.08131.62830.00130.01110.04140.0498-0.0264-0.1069-0.01820.0580.03430.1074-0.0005-0.00950.12250.00090.112570.891-1.488688.8588
21.9323-0.6849-0.79530.87850.41131.4201-0.03410.0034-0.14770.0584-0.01950.06050.06040.00550.0580.1248-0.00350.0010.10950.00550.111342.120725.54589.695
31.90741.19871.01421.35270.63621.36490.0169-0.12660.10960.059-0.02750.0985-0.0188-0.05630.00150.14390.00420.00740.1589-0.0110.119378.503736.823788.6788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA11 - 900
2X-RAY DIFFRACTION2chain BB11 - 900
3X-RAY DIFFRACTION3chain CC11 - 900

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